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<h3><u>BACKGROUND</u></h3>
P<sup>3</sup>DB was established with an overall objective to provide a resource 
of protein phosphorylation data from multiple plants. P<sup>3</sup>DB uses MySQL 
database to store phosphorylation data. With a PHP-based web interface, a user
can search, browse and download the phosphorylation data in the database.

<h3><u>SEARCH</u></h3>
A user can query the database for phosphoproteins or phosphopeptides. <br>
<ul>
<li> To search phosphoprotein,
  <ul>
    <li> On the query page, there are 4 options:
      <ol>
        <li>Peptide source organism: the organism from which the phospho-peptides come.
            see <a href="../help/note.php?item=pepsrc" class="notelink" onClick="return popup(this, 'notes')">note</a></li>
        <li>Research group or reference: 
           see <a href="../help/note.php?item=reference" class="notelink" onClick="return popup(this, 'notes')">a list of groups</a></li>
        <li>Protein accession number: 
            see <a href="../help/note.php?item=accession" class="notelink" onClick="return popup(this, 'notes')">supported accession types</a></li>
        <li>Protein description from other database.</li>
      </ol>
      <b><u>Note:</u></b> Query result will be generated according to all the field the user choose. E.g., if a user
            select "oilseed rape" as Peptide source organism and input "kinase" in Protein description, the query
            result will be all the phosphoprotein in the oilseed rape phosphorylation dataset with protein description
            contains "kinase".
    </li>
    <li>On the query result page, all relevant phosphoproteins are listed with several brief information:
      <ul>
        <li>Protein accession numbers hyperlinked to external database, e.g. UniProt (www.uniprot.org)</li>
        <li>Protein description byperlinked to the phosphoprotein page</li>
        <li>Peptide source organism</li>
        <li>Research groups or reference</li>
        <li>Protein score: see <a href="../help/note.php?item=score" class="notelink" onClick="return popup(this, 'notes')">Definition</a></li>
        <li>Spectrum count: see <a href="../help/note.php?item=spectrumcount" class="notelink" onClick="return popup(this, 'notes')">Definition</a></li>
      </ul>
      <b><u>Note:</u></b> the query result can be sorted by different criteria by click on the arraws.<br>
      &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<img src="./images/search_list_sort.jpg" />
    </li>
    <li>Clicking on the protein descriptions will take the user to the phosphoprotein page.</li>
  </ul>
</li>

<li> To search phosphopeptide,
  <ul>
    <li> On the query page, there are 3 options:
      <ol>
        <li>Peptide source organism</li>
        <li>Research group or reference</li>
        <li>Amino acid sequence: all peptides in the query result contained these amono acids in their sequences.
            If you would like to query out similar rather than exactly the same peptides, use phosphopeptide BLAST.</li>
      </ol>
    </li>
    <li>On the query result page, all relevant phosphopeptides are listed with information of peptide sequences,
        protein descriptions, source organisms, and research groups or references.</li>
  </ul>
</li>
</ul>

<h3><u>BLAST</u></h3>
To support advanced searching, a BLAST utility was integrated for querying phosphoproteins or phosphopeptides.
<ul>
<li>To search phosphoprotein
  <ul>
  <li>On the query page, a user need to,
    <ul>
      <li>input a protein sequence with length at least 5 (currently only multiple protein sequences are NOT supported),</li>
      <li>select dataset to BLAST against,</li> 
      <li>select proper E-values threshold (only BLAST hits with E-value below the select threshold will be listed in the result page).</li>
    </ul>
  </li>
  <li>On the query result page, the BLAST hits of phosphoproteins are listed with protein accessions, protein descriptions,
      source organisms and E-values.
  </li>
  </ul>
</li>

<li> To search phosphopeptide
  <ul>
  <li>On the query page, it is the same as in phosphoprotein BLAST.</li>
  <li>On the query result page 
    <ul>
    <li>The BLAST hits of phosphopeptides are listed with source organisms, protein descriptions,
      BLAST alignments and E-values.<br/>
      &nbsp;&nbsp;&nbsp;<img src="./images/blast_pep_list.jpg" />
    </li>
    <li>A BLAST alignments is comprised of query sequence, matching sequence and subject sequence (i.e. sequence in phosphopeptides).
         The subject sequences are hyperlinked to the phosphopeptide pages. The phosphorylation sites in the subject sequences are hyperlinked
         to the phosphorylation site pages. The corresponding residues in the query sequence of the phosphorylation sites are marked as red.
    </li>
    <li>Click on "Send to Phosphopeptide BLAST Browser" will send all the BLAST hits to the BLAST Browser.</li>
    </ul>
  </li>
  <li>Phosphopeptide BLAST Browser represents the phosphopeptide BLAST result graphically.
    <ul>
    &nbsp;&nbsp;&nbsp;<img src="./images/blast_browser.jpg" />
    <li>The query protein sequence is displayed. The phosphopeptides of the BLAST result is aligned to the query sequence and displayed 
        in different color by E-values according to the E-value color scheme.
    </li>
    <li>The phosphopeptides are linked to the phosphopeptide pages. The phosphorylation sites are linked to the site pages.
    </li>
    <li>The corresponding residues in the query sequence of the phosphorylation sites are marked as blue and linked to
        the corresponding phosphorylation sites.
    </li>
    </ul>
  </li>
  </ul>
</li>
</ul>

<h3><u>BROWSE</u></h3>
A user can browse the phosphoproteins according to different criteria:
<ul>
<li>A user can get the complete list of phosphoproteins in P<sup>3</sup>DB.</li>
<li>A user can get the phosphoprotein list for each source organism.</li>
<li>A user can get the phosphoprotein list for specific a gene ontology category.
  <ul>
  <li>Clicking on "+"/"-" will expand/shrink the branch.</li>
  <li>Clicking on "Browsing xx proteins" will list all phosphoproteins in the corresponding GO category.</li>
  &nbsp;&nbsp;&nbsp;<img src="./images/go_browse.jpg" />
  </ul>
</li>
</ul>
The phosphoprotein list page is similar to the result page for searching phophoproteins.

<h3><u>PHOSPHOPROTEIN PAGE</u></h3>
Phosphoprotein page lists the detailed information on a phosphoprotein, including:
<ul>
  <li>Accession: all protein accession numbers from
      <a href="../help/note.php?item=accession" class="notelink" onClick="return popup(this, 'notes')">supported accession types</a>
      will be listed if available.
  </li>
  <li>Description: protein description.
  </li>
  <li>Peptide source: the organism from which the phospho-peptides come.
      see <a href="../help/note.php?item=pepsrc" class="notelink" onClick="return popup(this, 'notes')">note</a>.
  </li>
  <li>Reference: research group or reference,
      see <a href="../help/note.php?item=reference" class="notelink" onClick="return popup(this, 'notes')">a list of groups</a>.
  </li>
  <li>GO slim: GO slim categories of the protein,
      see <a href="../help/note.php?item=goslim" class="notelink" onClick="return popup(this, 'notes')">notes</a>.
  </li>
  <li>Sequence: formated protein sequence with phosphorylation sites hyperlinked.</li>
</ul>

<h3><u>PHOSPHOPEPTIDE PAGE</u></h3>
Phosphopeptide page lists the available information on phosphopeptides, including:
<ul>
  <li>Sequence: peptide sequence with phosphorylation sites hyperlinked.</li>
  <li>Peptide source: the organism from which the phospho-peptides come.
      see <a href="../help/note.php?item=pepsrc" class="notelink" onClick="return popup(this, 'notes')">note</a>.
  </li>
  <li>Reference: research group or reference,
      see <a href="../help/note.php?item=reference" class="notelink" onClick="return popup(this, 'notes')">a list of groups</a>.
  </li>
  <li>Protein: corresponding phosphoprotein in which the phosphorylation occurs.
  </li>
  <li>Spectrum count: see <a href="../help/note.php?item=spectrumcount" class="notelink" onClick="return popup(this, 'notes')">definition</a>.
  </li>
  <li>MH+: peptide mass.
  </li>
  <li>Charge: the charge state of the peptide.
  </li>
  <li>Probability: The probability score is based on the probability that the peptide is a random match to the spectral data.
  </li>
  <li>Mascot score: see <a href="../help/note.php?item=mascotscore" class="notelink" onClick="return popup(this, 'notes')">definition</a>.
  </li>
  <li>Sf: the final score, see <a href="../help/note.php?item=sf" class="notelink" onClick="return popup(this, 'notes')">definition</a>.
  </li>
  <li>XCorr: see <a href="../help/note.php?item=xcorr" class="notelink" onClick="return popup(this, 'notes')">definition</a>.
  </li>
  <li>&Delta;Cn: see <a href="../help/note.php?item=deltacn" class="notelink" onClick="return popup(this, 'notes')">definition</a>.
  </li>
  <li>Mass error: see <a href="../help/note.php?item=masserr" class="notelink" onClick="return popup(this, 'notes')">definition</a>.
  </li>
  <li>Mass spectrum: link to the mass spectrum plot.
  </li>
  
</ul>

<h3><u>PHOSPHORYLATION SITE PAGE</u></h3>
Phosphorylation site page lists the available information on phosphorylation sites, including:
<ul>
  <li>Peptide source: the organism from which the phospho-peptides come.
      see <a href="../help/note.php?item=pepsrc" class="notelink" onClick="return popup(this, 'notes')">note</a>.
  </li>
  <li>Reference: research group or reference,
      see <a href="../help/note.php?item=reference" class="notelink" onClick="return popup(this, 'notes')">a list of groups</a>.
  </li>
  <li>Protein: corresponding phosphoprotein in which the phosphorylation occurs.
  </li>
  <li>Position: the position of the phosphorylation site in the phosphoprotein (start from 1).
  </li>
  <li>The amino acid (S/T/Y) of the phosphorylation site.
  </li>
  <li>Surrounding sequence: surrounding amino acids (+/-10) if applicable.
  </li>
  <li>Peptides: phosphopeptides containing this phosphorylation sites.<br/>
      Clicking "Show detail"/"Hide detail" to show/hide details on the peptide;
      Clicking on "More" to go the peptide page for additional information.
  </li>
</ul>

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